[2024-01-24 14:11:51,587] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:51,589] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:51,589] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf924d08-1d0b-4ce4-94fb-d71130894573/dqc_reference
[2024-01-24 14:11:52,872] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:52,873] [INFO] Task started: Prodigal
[2024-01-24 14:11:52,874] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ac338f7-f954-432d-82e0-9df9ca431f35/GCF_900660715.1_57675_H02-3_genomic.fna.gz | prodigal -d GCF_900660715.1_57675_H02-3_genomic.fna/cds.fna -a GCF_900660715.1_57675_H02-3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:11:54,360] [INFO] Task succeeded: Prodigal
[2024-01-24 14:11:54,361] [INFO] Task started: HMMsearch
[2024-01-24 14:11:54,361] [INFO] Running command: hmmsearch --tblout GCF_900660715.1_57675_H02-3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf924d08-1d0b-4ce4-94fb-d71130894573/dqc_reference/reference_markers.hmm GCF_900660715.1_57675_H02-3_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:11:54,640] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:11:54,642] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0ac338f7-f954-432d-82e0-9df9ca431f35/GCF_900660715.1_57675_H02-3_genomic.fna.gz]
[2024-01-24 14:11:54,653] [INFO] Query marker FASTA was written to GCF_900660715.1_57675_H02-3_genomic.fna/markers.fasta
[2024-01-24 14:11:54,653] [INFO] Task started: Blastn
[2024-01-24 14:11:54,654] [INFO] Running command: blastn -query GCF_900660715.1_57675_H02-3_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf924d08-1d0b-4ce4-94fb-d71130894573/dqc_reference/reference_markers.fasta -out GCF_900660715.1_57675_H02-3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:11:57,513] [INFO] Task succeeded: Blastn
[2024-01-24 14:11:57,539] [INFO] Selected 8 target genomes.
[2024-01-24 14:11:57,539] [INFO] Target genome list was writen to GCF_900660715.1_57675_H02-3_genomic.fna/target_genomes.txt
[2024-01-24 14:11:57,548] [INFO] Task started: fastANI
[2024-01-24 14:11:57,549] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ac338f7-f954-432d-82e0-9df9ca431f35/GCF_900660715.1_57675_H02-3_genomic.fna.gz --refList GCF_900660715.1_57675_H02-3_genomic.fna/target_genomes.txt --output GCF_900660715.1_57675_H02-3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:11:58,762] [INFO] Task succeeded: fastANI
[2024-01-24 14:11:58,763] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf924d08-1d0b-4ce4-94fb-d71130894573/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:11:58,763] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf924d08-1d0b-4ce4-94fb-d71130894573/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:11:58,810] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:11:58,810] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:11:58,811] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Metamycoplasma arthritidis	strain=NCTC10162	GCA_900660715.1	2111	2111	type	True	100.0	268	268	95	conclusive
Metamycoplasma salivarium	strain=ATCC 23064	GCA_000485555.1	2124	2124	type	True	78.1227	50	268	95	below_threshold
Metamycoplasma salivarium	strain=NCTC10113	GCA_900660445.2	2124	2124	type	True	77.8595	55	268	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:11:58,813] [INFO] DFAST Taxonomy check result was written to GCF_900660715.1_57675_H02-3_genomic.fna/tc_result.tsv
[2024-01-24 14:11:58,814] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:11:58,814] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:11:58,814] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf924d08-1d0b-4ce4-94fb-d71130894573/dqc_reference/checkm_data
[2024-01-24 14:11:58,823] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:11:58,838] [INFO] Task started: CheckM
[2024-01-24 14:11:58,838] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900660715.1_57675_H02-3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900660715.1_57675_H02-3_genomic.fna/checkm_input GCF_900660715.1_57675_H02-3_genomic.fna/checkm_result
[2024-01-24 14:12:18,793] [INFO] Task succeeded: CheckM
[2024-01-24 14:12:18,794] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:12:18,830] [INFO] ===== Completeness check finished =====
[2024-01-24 14:12:18,830] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:12:18,831] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900660715.1_57675_H02-3_genomic.fna/markers.fasta)
[2024-01-24 14:12:18,831] [INFO] Task started: Blastn
[2024-01-24 14:12:18,832] [INFO] Running command: blastn -query GCF_900660715.1_57675_H02-3_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf924d08-1d0b-4ce4-94fb-d71130894573/dqc_reference/reference_markers_gtdb.fasta -out GCF_900660715.1_57675_H02-3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:20,579] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:20,583] [INFO] Selected 11 target genomes.
[2024-01-24 14:12:20,583] [INFO] Target genome list was writen to GCF_900660715.1_57675_H02-3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:12:20,600] [INFO] Task started: fastANI
[2024-01-24 14:12:20,601] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ac338f7-f954-432d-82e0-9df9ca431f35/GCF_900660715.1_57675_H02-3_genomic.fna.gz --refList GCF_900660715.1_57675_H02-3_genomic.fna/target_genomes_gtdb.txt --output GCF_900660715.1_57675_H02-3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:12:22,909] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:22,933] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:12:22,934] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_900660715.1	s__Metamycoplasma arthritidis	100.0	268	268	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_900660445.2	s__Metamycoplasma salivarium	77.8595	55	268	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003332325.1	s__Metamycoplasma phocidae	77.6597	53	268	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:12:22,944] [INFO] GTDB search result was written to GCF_900660715.1_57675_H02-3_genomic.fna/result_gtdb.tsv
[2024-01-24 14:12:22,945] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:12:22,948] [INFO] DFAST_QC result json was written to GCF_900660715.1_57675_H02-3_genomic.fna/dqc_result.json
[2024-01-24 14:12:22,949] [INFO] DFAST_QC completed!
[2024-01-24 14:12:22,949] [INFO] Total running time: 0h0m31s